Validate Olink Data

This function validates Olink data based on a set of criteria, including folder structure, metadata, and file contents. It supports optional functionalities like creating a PDF report and DMAQC validation (data only available at the BIC)

Usage

validate_olink(
  input_results_folder,
  cas,
  return_n_issues = FALSE,
  full_report = FALSE,
  f_proof = FALSE,
  printPDF = FALSE,
  out_qc_folder = NULL,
  dmaqc_shipping_info = NULL,
  dmaqc_phase2validate = FALSE,
  validate_uniprot = FALSE,
  verbose = TRUE
)

Arguments

input_results_folder

A string representing the path to the folder containing Olink results to be validated.

cas

A character string indicating the CAS number.

return_n_issues

Logical; if TRUE, the function returns the number of detected issues.

full_report

Logical; if TRUE, generates a full report of the validation process.

f_proof

Logical; if TRUE, generates proof plots for data validation.

printPDF

Logical; if TRUE and f_proof is TRUE, saves the plots to a PDF file, and in such case, then provide the desired path to output the PDF file in the argument out_qc_folder

out_qc_folder

Optional; a string specifying the path to the folder where output PDF should be saved (only if printPDF = TRUE). Default: current working directory

dmaqc_shipping_info

(char) File path to the DMAQC file. Only the BIC can use this argument

dmaqc_phase2validate

(char) Provide phase to validate. This argument is not required since it should be extracted from the input folder or from the new required file metadata_phase.txt. Please, ignore. However, if this argument is provided, it will take priority and this will be the phase.

validate_uniprot

Logical; if TRUE, validates against the UniProt database.

verbose

Logical; if TRUE, prints detailed messages during validation.

Value

Depending on the settings, this function may return the number of issues found, generate reports or plots, or simply perform the validation without returning anything.

Examples

if (FALSE) { # \dontrun{
validate_olink("/path/to/results", cas = "broad_rg", return_n_issues = TRUE)
} # }